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Cadmium in PDB 3rav: Horse Spleen Apo-Ferritin with Bound Pentobarbital

Protein crystallography data

The structure of Horse Spleen Apo-Ferritin with Bound Pentobarbital, PDB code: 3rav was solved by S.H.Oakley, L.S.Vedula, J.Xi, R.Liu, R.G.Eckenhoff, P.J.Loll, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.62 / 1.90
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 182.480, 182.480, 182.480, 90.00, 90.00, 90.00
R / Rfree (%) 17.4 / 20.8

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Horse Spleen Apo-Ferritin with Bound Pentobarbital (pdb code 3rav). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 6 binding sites of Cadmium where determined in the Horse Spleen Apo-Ferritin with Bound Pentobarbital, PDB code: 3rav:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6;

Cadmium binding site 1 out of 6 in 3rav

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Cadmium binding site 1 out of 6 in the Horse Spleen Apo-Ferritin with Bound Pentobarbital


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Horse Spleen Apo-Ferritin with Bound Pentobarbital within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd175

b:30.0
occ:0.52
OD2 A:ASP80 2.3 27.7 1.0
OD1 A:ASP80 2.8 21.5 1.0
CG A:ASP80 2.9 24.2 1.0
CB A:ASP80 4.4 22.2 1.0
O A:HOH255 4.8 29.7 1.0

Cadmium binding site 2 out of 6 in 3rav

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Cadmium binding site 2 out of 6 in the Horse Spleen Apo-Ferritin with Bound Pentobarbital


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Horse Spleen Apo-Ferritin with Bound Pentobarbital within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd176

b:41.8
occ:0.39
O A:HOH285 2.2 42.5 1.0
O A:HOH276 2.2 29.2 1.0
OE1 A:GLU56 2.5 45.7 1.0
OE2 A:GLU60 2.6 37.7 1.0
OE1 A:GLU60 2.6 31.8 1.0
OE2 A:GLU57 2.7 40.0 1.0
CD A:GLU60 3.0 32.2 1.0
CD A:GLU56 3.5 39.9 1.0
CD A:GLU57 3.8 36.1 1.0
CG A:GLU56 3.8 31.1 1.0
OE1 A:GLU57 4.2 41.8 1.0
O A:HOH195 4.3 43.8 1.0
CG A:GLU60 4.5 23.9 1.0
OE2 A:GLU56 4.7 41.3 1.0
O A:HOH283 4.7 42.2 1.0
O A:HOH341 4.7 40.3 1.0

Cadmium binding site 3 out of 6 in 3rav

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Cadmium binding site 3 out of 6 in the Horse Spleen Apo-Ferritin with Bound Pentobarbital


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Horse Spleen Apo-Ferritin with Bound Pentobarbital within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd177

b:55.2
occ:0.49
O A:HOH283 2.4 42.2 1.0
OE1 A:GLU53 2.6 45.6 1.0
OE2 A:GLU56 2.7 41.3 1.0
OE2 A:GLU53 2.8 42.8 1.0
CD A:GLU53 3.1 40.0 1.0
OE1 A:GLU56 3.2 45.7 1.0
CD A:GLU56 3.3 39.9 1.0
CG A:GLU53 4.6 30.2 1.0
O A:HOH341 4.7 40.3 1.0
CG A:GLU56 4.7 31.1 1.0

Cadmium binding site 4 out of 6 in 3rav

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Cadmium binding site 4 out of 6 in the Horse Spleen Apo-Ferritin with Bound Pentobarbital


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Horse Spleen Apo-Ferritin with Bound Pentobarbital within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd178

b:45.8
occ:0.23
OD1 A:ASP127 2.8 41.4 1.0
CG A:ASP127 4.0 37.7 1.0
OE1 A:GLU130 4.2 36.7 1.0
CB A:ASP127 4.8 31.4 1.0
OD2 A:ASP127 4.9 41.8 1.0
O A:ASP127 4.9 25.1 1.0
CD A:CD179 4.9 48.3 0.3
CB A:SER131 5.0 39.3 1.0
CA A:ASP127 5.0 25.9 1.0

Cadmium binding site 5 out of 6 in 3rav

Go back to Cadmium Binding Sites List in 3rav
Cadmium binding site 5 out of 6 in the Horse Spleen Apo-Ferritin with Bound Pentobarbital


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Horse Spleen Apo-Ferritin with Bound Pentobarbital within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd179

b:48.3
occ:0.33
O A:HOH277 2.3 43.2 1.0
OE1 A:GLU130 2.5 36.7 1.0
CD A:GLU130 3.2 32.5 1.0
OE2 A:GLU130 3.2 28.5 1.0
CG A:GLU130 4.6 29.1 1.0
CD A:CD178 4.9 45.8 0.2

Cadmium binding site 6 out of 6 in 3rav

Go back to Cadmium Binding Sites List in 3rav
Cadmium binding site 6 out of 6 in the Horse Spleen Apo-Ferritin with Bound Pentobarbital


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Horse Spleen Apo-Ferritin with Bound Pentobarbital within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd182

b:75.8
occ:0.82
OE2 A:GLU11 2.7 34.2 1.0
OE1 A:GLU11 2.7 22.4 1.0
CD A:GLU11 3.0 31.6 1.0
O A:HOH263 3.3 31.7 1.0
OG1 A:THR10 4.1 28.0 1.0
CG A:GLU11 4.5 25.0 1.0
NE2 A:GLN120 4.7 30.2 1.0
OE1 A:GLN120 4.7 32.1 1.0
CB A:SER9 4.9 20.9 1.0

Reference:

S.H.Oakley, L.S.Vedula, J.Xi, R.Liu, R.G.Eckenhoff, P.J.Loll. High Resolution View of Barbiturate Recognition By A Protein Binding Site To Be Published.
Page generated: Sun Jan 24 09:56:00 2021

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